Five probes including four that contained isoprenoid chain were synthesized. These probes were assembled onto the gold-coated quartz crystal chips for analysis of their interactions with four yeast proteins by using the quartz crystal microbalance technology. Results showed that 3-phosphoglycerate phosphokinase and triosephosphate isomerase had clear interactions with certain probes, while glutathione reductase and phosphoglucose isomerase gave much lower interaction signals. It also suggested that 3-phosphoglycerate phosphokinase had two sites interacting with the probe attached with a geranyl moiety. Further molecule simulation experiments provided supportive information on these intermolecular interactions. Together, our data suggested that there are hydrophobic interactions, with relatively good selectivity, between isoprenoid chain and proteins. (C) 2013 Elsevier Ltd. All rights reserved.